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CHE 541 > 4 - Tertiary Structure and Fibrous Proteins > Flashcards

4 - Tertiary Structure and Fibrous Proteins Flashcards

1
Q

Which amino acids are fluorescent?

A

Trp and Tyr

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2
Q

What does the extinction coefficient tell you?

A

How easily a molecule catches photons (absorbance)

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3
Q

Which amino acid has the highest extinction coefficient at 280 nm?

A

Trp

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4
Q

What does it mean to be fluorescent?

A

It can release an electron when a photon is absorbed

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5
Q

How come Trp and Tyr are fluorescent?

A

They are rigid (aromatic rings) to not move around, so they release energy

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6
Q

What technique uses the fluorescence of Trp?

A

FRET

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7
Q

What is Trp’s fluorescence dependent on?

A

Its microenvironment

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8
Q

What happens if Trp is in a more hydrophobic environment?

A

Higher energy –> shorter wavelength

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9
Q

What happens if Trp is in a more hydrophilic environment?

A

Lower energy -> longer wavelength

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10
Q

What is protein primary structure?

A

Covalent amino acid sequence

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11
Q

What is protein secondary structure?

A

Alpha helix and beta sheet stabilized by noncovalent interactions

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12
Q

What is protein tertiary structure?

A

Folding of local secondary structure to form final folded structure

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13
Q

What is protein quaternary structure?

A

Association of monomers to oligomers

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14
Q

What is a polymer chemist’s view on a protein?

A

View as a polymer with nodes that can rotate to give the lowest energy

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15
Q

What is a peptide bond?

A

The amide bond in the polypeptide chain

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16
Q

What is the configuration of the peptide bond?

A

Planar

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17
Q

How come the peptide bond is planar?

A

It has double bond character, so it cannot rotate

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18
Q

How much shorter is a peptide bond compared to a C-N bond?

A

0.13 A shorter

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19
Q

How many J of resonance energy is in a peptide bond?

A

85 kJ/mol

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20
Q

Are peptide bonds usually trans or cis?

A

Trans

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21
Q

Which amino acid can have cis conformation?

A

Pro

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22
Q

How come Pro can be cis?

A

It has a ring to tie back the polypeptide, and help lock it into the cis conformation

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23
Q

What is the trans:cis ratio of an amino acid that proceeds Pro?

A

10:1 - 20:1

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24
Q

Why would a cis bond proceed a Pro?

A

It can break helices and beta-sheets by disrupting H-bonds and sterics

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25
Q

How can an amino acid go from trans to cis?

A

Through enzymes

26
Q

How do isomerases for trans to cis amino acids work?

A

They form a tetrahedral intermediate to allow for free rotation before locking it back into place

27
Q

What does peptidyl prolyl cis-trans isomerase do?

A

Converts trans-Pro into cis-Pro

28
Q

By how much does peptidyl prolyl cis-trans isomerase lower the activation energy?

A

By 6-8 kcal/mol

29
Q

What dictates polypeptide conformation?

A

Dihedral angles around Ca-N and Ca-C=O bonds

30
Q

What is the phi angle?

A

Angle around Ca-N

31
Q

What is the psi angle?

A

Angle around Ca-C=O

32
Q

What does a Ramachandran plot describe?

A

The steric constraints on phi/psi that limit the conformational range of polypeptide backbone

33
Q

What is the largest area on the Ramachandran plot?

A

Beta-sheet

34
Q

What is the smallest area on the Ramachandran plot?

A

Alpha helix

35
Q

What angles lead to a beta-sheet?

A

phi: -180 to -60, psi: 30 to 180

36
Q

What angles lead to an alpha helix?

A

phi: -30 to -180, psi: -30 to -70

37
Q

Which amino acid has the most conformational freedom?

A

Gly

38
Q

What does the Ramachandran plot look like for Gly?

A

Large availability around the corners

39
Q

Which amino acid has the least conformational freedom?

A

Pro

40
Q

What does the Ramachandran plot look like for Pro?

A

One small strip

41
Q

How does a Ramachandran plot explain an alpha helix?

A

Steric cliash at phi = 180, psi = 0, so rotate phi to releave steric clash

42
Q

What shape are the majority of alpha helices?

A

Right handed

43
Q

What H-bonds are present in an alpha helix?

A

Backbone of C=O with NH 4 amino acids down

44
Q

What dipoles are present in an alpha helix?

A

Along amide bond, aligned to reinforce dipoles (electrostatics)

45
Q

What are the common configurations for an alpha helix?

A

Phi = 60, psi = -50, 3.6 amino acids per turn

46
Q

What are some other types of alpha helixes?

A

3/10, pi, and left-handed

47
Q

Which amino acids are preferred in an alpha helix?

A

Ala, Glu, Leu, Met

48
Q

Which amino acids are not preferred in an alpha helix?

A

Pro, Gly, Ser, Val, Ile, Thr

49
Q

How are the R groups oriented in an alpha helix?

A

Extended away from the helix center

50
Q

What is needed for an H-bond?

A

A lone pair for an acceptor, and an H for a donor

51
Q

Where are the weak parts of an alpha helix and why?

A

The ends, because there are unfulfilled H-bonds at the end

52
Q

How can the ends of an alpha helix be stabilized?

A

By capping

53
Q

Which amino acids are common for N-capping?

A

Ser, Asp, Thr, Asn

54
Q

What makes Ser, Asp, Thr, and Asn good for N-capping?

A

They have a lone pair (H-bond acceptor) in the right location for the NH donor

55
Q

Which amino acids are common for C-capping?

A

Gly

56
Q

What makes Gly good for C-capping?

A

It can adopt a left handed conformation to allow for NH to be a donor for the two helical carbonyls

57
Q

Where does the dipole originate in an alpha helix?

A

The amide bond (0.5-0.7 unit charge on N-terminus)

58
Q

True or false: alpha helices can be ampipathic?

A

True: they can have distinct faces

59
Q

How can you tell if an alpha helix is ampipathic?

A

By drawing a helical wheel diagram

60
Q

How do you draw a helical wheel diagram?

A

By drawing each amino acid 100 degrees (a little more than 90, 3.6 amino acids per turn) from the previous one

CHE 541 (20 decks)

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